https://github.com/thehyve/tmtk

tranSMART Arborist ETL toolkit
https://github.com/thehyve/tmtk

data-curation data-modeling jupyter-notebook transmart

Last synced: about 2 months ago
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tranSMART Arborist ETL toolkit

• Host: GitHub
• URL: https://github.com/thehyve/tmtk
• Owner: thehyve
• License: lgpl-3.0
• Archived: true
• Created: 2016-04-11T09:13:11.000Z (over 8 years ago)
• Default Branch: develop
• Last Pushed: 2020-07-31T15:02:59.000Z (over 4 years ago)
• Last Synced: 2024-09-24T22:04:10.308Z (about 2 months ago)
• Topics: data-curation, data-modeling, jupyter-notebook, transmart
• Language: Python
• Homepage: https://pypi.org/project/tmtk/
• Size: 3.89 MB
• Stars: 6
• Watchers: 11
• Forks: 4
• Open Issues: 5
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE.txt

Awesome Lists containing this project

README

        
====

tmtk

====

Master:

.. image:: https://travis-ci.org/thehyve/tmtk.svg?branch=master

    :target: https://travis-ci.org/thehyve/tmtk

.. image:: https://codecov.io/gh/thehyve/tmtk/branch/master/graph/badge.svg

    :target: https://codecov.io/gh/thehyve/tmtk

.. image:: https://readthedocs.org/projects/tmtk/badge/?version=latest

    :target: http://tmtk.readthedocs.io/en/latest/?badge=latest

    :alt: Documentation Status

Develop:

.. image:: https://travis-ci.org/thehyve/tmtk.svg?branch=develop

    :target: https://travis-ci.org/thehyve/tmtk

.. image:: https://codecov.io/gh/thehyve/tmtk/branch/develop/graph/badge.svg

    :target: https://codecov.io/gh/thehyve/tmtk

Anaconda Cloud latest package:

.. image:: https://anaconda.org/conda-forge/tmtk/badges/version.svg

    :target: https://anaconda.org/conda-forge/tmtk

A toolkit for ETL curation for the tranSMART data warehouse. The

TranSMART curation toolkit (``tmtk``) can be used to edit and validate

studies prior to loading them with `transmart-batch`_.

For general documentation visit `readthedocs`_.

Installation

------------

Installing via Anaconda Cloud or Pip package managers

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Anaconda:

.. code:: sh

    conda install -c conda-forge tmtk

Pip:

.. code:: sh

    pip install tmtk

Installing manually

^^^^^^^^^^^^^^^^^^^

Initialize a virtualenv

~~~~~~~~~~~~~~~~~~~~~~~

.. code:: bash

    python3 -m venv env

    source env/bin/activate

Installation from source

~~~~~~~~~~~~~~~~~~~~~~~~

To install *tmtk* and all dependencies into your Python environment,

and enable the Arborist Jupyter notebook extension, run:

.. code:: sh

    pip install -r requirements.txt

    python setup.py install

or if you want to run the tool from code in development mode:

.. code:: sh

    pip install -r requirements.txt

    python setup.py develop

    jupyter-nbextension install --py tmtk.arborist

    jupyter-serverextension enable tmtk.arborist

Requirements

^^^^^^^^^^^^

The dependencies are in ``requirements.txt``,

optional dependencies are in ``requirements-dev.txt``.

Licence

-------

LGPL-3.0

.. _transmart-batch: https://github.com/thehyve/transmart-batch/

.. _virtualenvwrapper: https://virtualenvwrapper.readthedocs.io

.. _readthedocs: https://tmtk.readthedocs.io/en/latest/

.. _examples: examples